I just generated a 5 million line file that approximates your format:

#! perl -slw
use strict;

for( 1 .. 5e6 ) {
    my $n1 = int( rand 100 );
    my $n2 = int( rand 1e6 );

    printf "w\t%d\t%d\t75\t75M\t0\n", $n1, $n2;
    printf "c\t%d\t%d\t75\t75M\t0\n", $n1, $n2 - int( rand 1000 ) + 50
+0;

}
__END__
C:\test>head 1166792.dat
w       70      437286  75      75M     0
c       70      437579  75      75M     0
w       50      852386  75      75M     0
c       50      852473  75      75M     0
w       45      45196   75      75M     0
c       45      45695   75      75M     0
w       83      1739    75      75M     0
c       83      1590    75      75M     0
w       31      838500  75      75M     0
c       31      838902  75      75M     0
[download]

And wrapped your posted snippet up to allow it to run:

#! perl -slw
use strict;

open my $IN2, '<', '1166792.dat' or die $!;

my( %store, %Tally );

while (<$IN2>) {
    chomp $_;
    next if eof;
    my @F2      = split( "\t", $_ );          #Split each tab-delimite
+d field
    my $partner = <$IN2>;
    my @F3      = split( "\t", $partner );    #Split each tab-delimite
+d field
    $store{ ( abs( $F2[2] - $F3[2] ) + 1 ) }++;
    ( $F2[2], $F3[2] ) = ( $F3[2], $F2[2] ) if $F2[2] > $F3[2];
    $Tally{ $F2[1] }{ $F2[2] }{ $F3[2] }++;
}

foreach my $key ( sort { $a <=> $b } keys %store ) {
    print "$key\t$store{$key}\n";
}

foreach my $chr ( sort { $a <=> $b } keys %Tally ) {
    foreach my $value1 ( sort { $a <=> $b } keys %{ $Tally{$chr} } ) {
        foreach my $value2 ( sort { $a <=> $b } keys %{ $Tally{$chr}{$
+value1} } ) {
            print "$chr\t$value1\t$value2\t$Tally{$chr}{$value1}{$valu
+e2}\n";
        }
    }
}
[download]

And it runs to completion under 5.22 using just under 1.2GB.

Unless you're on a very memory constrained system, memory isn't the problem. Do you have somewhere you can post your failing datafile (zipped.)?

I wonder if it is indeed a subtle error with the input file then - although that would be quite odd as every line in it was printed by Perl in the exact same manner. I've uploaded my failing file here:

https://www.dropbox.com/s/mofwaf7iiuif0ur/Example.txt.zip?dl=0

Let me know if that is not suitable/inaccessible. Should be able to download without logging in.

Hm. Other than having to add a line to discard the header; your file processed to completion without error.

Two possibilities:

1. (Unlikely) The data file is corrupted on disk with a bad block or similar.

   Copy the file to another name (or unzip the zip you posted) and try that.

2. (More unlikely). Your perl installation is broken.

   Install another version and try again.

Beyond those we're into a world of even more speculative guessing.

---

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority". I knew I was on the right track :)

In the absence of evidence, opinion is indistinguishable from prejudice. Not understood.

Ignore this: That was harangzsolt33.

You're not the guy I saw mention last week some time he was using tinyperl?

Use of uninitialized value in subtraction (-) at line 117, <$IN2> line
+ 4148567.
Use of uninitialized value in numeric gt (>) at line 118, <$IN2> line 
+4148567.
Use of uninitialized value $F2[2] in hash element at line 119, <$IN2> 
+line 4148567.
Argument "" isn't numeric in sort at line 127, <$IN2> line 4148567.
[download]

Instead of randomly reshuffling the file, could you not extract that 1 line (head -4148567 <file> | tail -1) and then run your script against that 1 line? If I head to guess, seeing that $F[2] is the culprit, I'm guessing you have a double tab on that particular line.

update:Nevermind ... I shouldn't answer questions without first reading the whole thing and second not having finished my morning cup of coffee.